MmuINT0139728 @ mm10
Intron Retention
Gene
ENSMUSG00000032511 | Scn5a
Description
sodium channel, voltage-gated, type V, alpha [Source:MGI Symbol;Acc:MGI:98251]
Coordinates
chr9:119533663-119534734:-
Coord C1 exon
chr9:119534555-119534734
Coord A exon
chr9:119534035-119534554
Coord C2 exon
chr9:119533663-119534034
Length
520 bp
Sequences
Splice sites
5' ss Seq
TTGGTAATC
5' ss Score
3.39
3' ss Seq
CACCCTCCCTGTGCCCTCAGAAT
3' ss Score
10.85
Exon sequences
Seq C1 exon
GCTCTCACCATCAGGGGCGTGGATACTGTGTCCCGTAGCTCTCTGGAGATGTCTCCTTTGGCCCCAGTAACCAACCATGAGAGAAGGAGCAAGAGGAGGAAACGACTGTCTTCAGGGACAGAGGATGGCGGAGATGACAGGCTCCCCAAGTCGGACTCAGAAGACGGTCCCAGAGCATTG
Seq A exon
GTAATCCTGACGTGGTTCTGGCCTCTGCAAAACCCATCATGATGGCCCCCACCCCACCCCCAGTGTGGTCACAGCCTTAAGCTTAGTCTCCAAGAAAGGCATGCTTGGACCCCTCTCATCCCTTCCAGTTTCCCTTAGTCATTCTTAAATTGGGGGAGAGCTAGGGCAGGTTTGTGTGTTAATGCTGCCTCCTACCTGGAAATAGTCCTCAAGTACAGGGACCAGCACTGGGAGTGGGGGCCTGTGGTGTGGGGTGATAGGGGCCCAAGTACTGGTCCTAGCTCTTCTGCCCAGCCTAGCCCCACCCCCAGGCCCAGAGCAGCATCAGAGTCAAACCCAGAGATGCAGGGGCGAAGTGAATAGAGGACCCAGAAGATGCAGGGGACACCCCATCTCTTCCTAAGCACCCACCCACCCCCGCTGTGGCCAGCAGAAGTGCTCTCAGAAGTGAGCTGAGCTGATACTTTGGCTGAAGCAGAGACCAAGCCCTGTGGGTCACGCACCCTCCCTGTGCCCTCAG
Seq C2 exon
AATCAGCTCAGCCTCACCCATGGGCTCAGCCGGACATCCATGAGGCCCCGCTCCAGCCGAGGGAGCATTTTCACATTCCGGCGACGGGACCAAGGCTCCGAGGCAGATTTTGCAGATGACGAGAACAGTACAGCAGGAGAGAGCGAGAGCCACCGCACATCGCTGCTGGTGCCCTGGCCCCTGCGCCGTCCCAGCACCCAAGGGCAGCCCGGCTTTGGAACCTCAGCTCCTGGTCATGTCCTCAATGGCAAAAGAAACAGCACCGTGGACTGCAATGGGGTGGTTTCCTTGCTGGGGGCAGGGGACGCAGAGGCCACCTCTCCAGGGAGCCACCTTCTCCGCCCTATAGTGCTGGACAGACCCCCAGACACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032511:ENSMUST00000117911:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.767 A=NA C2=0.895
Domain overlap (PFAM):
C1:
PF119333=DUF3451=PU(21.6=75.0)
A:
NA
C2:
PF119333=DUF3451=FE(59.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGAGCAAGAGGAGGAAACGA
R:
GCCATTGAGGACATGACCAGG
Band lengths:
345-865
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types